Princeton NA&P Lab

The Princeton NA&P Lab dataset includes anatomical and diffusion data from 2 rhesus monkeys.

Usage Agreement

Creative Commons – Attribution-NonCommercial Share Alike (CC-BY-NC-SA)- Standard INDI data sharing policy. Prohibits use of the data for commercial purposes.

Species

Macaca mulatta

Scanner Specifications

• Scanner type: Siemens Prisma VE11C 3T
• Coil: Siemens Loop Coil, Large (11cm)
• Stereotax: Kopf 1430M

Sample Description

• Sample size: 2
• Age distribution: 3 years
• Weight distribution: 4.7-5.5 kg
• Sex distribution: both male

Click here for the full sample description (.csv)

Scan Procedures and Parameters

Ethics approval: All methods and procedures were approved by the Princeton University IACUC.

Animal care and housing: Princeton University is staffed with 2 full-time veterinarians and an extensive staff of veterinary and husbandry technicians. Animals are pair-housed and receive environmental enrichment consisting of toys, foraging devices, cable TV, and access to a large enrichment space.

Any applicable training: none

Anesthesia procedures: For structural and diffusion sessions (sessions 1-3), animals were first sedated with ketamine (10mg/kg IM) and maintained with isoflurane gas (2.5-3.0%). For resting state fMRI (session 4), animals were first sedated with ketamine (10mg/kg IM) and xylazine (0.5mg/kg IM), and sedation was maintained with additional ketamine doses as needed to complete the session without head or body motion.

Head fixation: Kopf 1430M MRI Stereotaxic frame

Position in scanner and procedure used: Animals were placed in the “sphinx” position.

Contrast agent: None

Physiological monitoring: For all scan sessions (1-4), Siemens wireless physiology sensors were used to monitor EKG, pulse, and respiratory rate. Body temperature was monitored using a fiber optic probe (FOTS100, BioPac Systems Inc.). For structural and diffusion sessions (sessions 1-3), an InVivo 3150 MRI Patient Monitor was used to monitor SpO2 and end tidal CO2 during structural and diffusion scan sessions.

Additional procedures: For structural and diffusion sessions (sessions 1-3), artificial ventilation was used to maintain normocapnia. For all scan sessions (1-4), normothermia was maintained using blankets and a warm water re-circulating pump (Stryker/Gaymar TP700 T/Pump) modified with long tubing to reach the MRI bore.

Scan sequences

• Structural (Session 1):
  • T1w-MPRAGE
    • Voxel resolution: 0.5 x 0.5 x 0.5mm
    • TE: 2.32ms
    • TR: 2700ms
    • TI: 850ms
    • Number of slices: 240
    • FOV/Matrix: 128mm/256
    • Flip angle: 9°
    • Averages: 3
    • Scans: 3
  • T2w-SPACE
    • Voxel resolution: 0.5 x 0.5 x 0.5mm
    • TE: 398ms
    • TR: 3500ms
    • Number of slices: 240
    • FOV/Matrix: 128mm/256
    • Averages: 1
    • Scans: 1
• Diffusion-weighted (Session 2):
• Voxel resolution: 1 x 1 x 1mm
• TE: 83ms
• TR: 7200ms
• Number of slices: 50
• FOV/Matrix: 96mm/96
• Phase encode direction: RL or LR
• B-values: 1250 and 2500 s/mm²
• Directions: 150 (14 b=0; 50 directions @ b=1250; 100 directions @ b=2500)
• Scans: 10 (half under reversed polarity)
• Diffusion-weighted (Session 3):
• Voxel resolution: 1 x 1 x 1mm
• TE: 83ms
• TR: 8000ms
• Number of slices: 50
• FOV/Matrix: 96mm/96
• Phase encode direction: RL or LR
• B-values: 850, 1650, 2500 s/mm²
• Directions: 271 (18 b=0; 91 directions @ b=850; 90 directions @ b=1650; 90 directions @ b=2500)
• Scans: 4 (half under reversed polarity)
• Resting State fMRI (Session 4):
• Voxel resolution: 1.65 x 1.65 x 1.65mm
• TE: 26.20ms
• TR: 1975ms
• Number of slices: 32
• FOV/Matrix: 99mm/60
• Phase encode direction: RL or LR
• Flip angle: 70 deg
• Measurements: 456
• Scans: 4 (half under reversed polarity)

Experimental Protocol

Click here for scan parameters from the scanner console (pdf). Below are some details not captured in the pdf:

• Session 1 (anat) contains multiple T1 scans and a T2 scan. A vitamin E marker was placed over the animal’s right ear. Sessions 2, 3 and 4 (diffusion and fMRI) each have a T1 scan for those sessions, but no vitamin E markers.
• Session 2 (diffusion) contains a T1 scan, and 10 diffusion datasets, half of which are collected under reversed phase-encoding direction (RL or LR). Each dataset is in its own subfolder. In each of those folders are the diffusion data with their respective bvecs and bvals tables. The diffusion data is a 2-shell 150-direction scheme, where 50 directions are acquired at b=1250, and 100 directions are acquired at b=2500. In addition 14 b=0 scans are acquired.
• Session 3 (diffusion) contains a T1 scan, and 4 diffusion datasets, half of which are collected under reversed phase-encoding (RL or LR). Each dataset is in its own subfolder. In each of those folders are the diffusion data with their respective bvecs and bvals tables. The diffusion data is a 3-shell 271-direction scheme, where 91 directions are acquired at b=850, 90 directions are acquired at b=1650, and 90 directions are acquired at b=2500. In addition 18 b=0 scans are acquired.
• Session 4 (resting state fMRI) contains a T1 scan, and 4 resting state scans, half of which are collected under reversed phase-encoding (RL or LR). Each scan is in its own subfolder. EPI and spin echo scans were collected using sequences provided by C2P agreement with University of Minnesota (release R016a) allowing matrix sizes < 64 and recording of physiological signals. Physiological signal log files are included as well. Spin echo scans collected under reversed phase-encoding are also in sub-folders.

Personnel

• Mark Pinsk
• Sabine Kastner

Acknowledgements

This data repository was supported by the following grants: NIMH 1P50MH109429; NIMH R01MH064043; NEI R01EY017699.

Downloads

Click here to download the data. Users will first be prompted to log on to NITRC and will need to register with the 1000 Functional Connectomes Project website on NITRC to gain access to the PRIME-DE datasets.